diff --git a/news/changelog-1.12.md b/news/changelog-1.12.md
index 2c099415446..c92f446eb60 100644
--- a/news/changelog-1.12.md
+++ b/news/changelog-1.12.md
@@ -16,6 +16,7 @@ All changes included in 1.12:
 
 ### `html`
 
+- ([#9606](https://github.com/quarto-dev/quarto-cli/issues/9606)): Fix `format-links` entries written as `{format, text}` adding a second, default link for the same format instead of renaming its link.
 - ([#15269](https://github.com/quarto-dev/quarto-cli/pull/15269)): Fix `link-external-newwindow` overriding a `target` set explicitly on a link. (author: @mcanouil)
 
 ### `pdf`
diff --git a/src/format/html/format-html-links.ts b/src/format/html/format-html-links.ts
index f7ea856c92c..22f5565f16f 100644
--- a/src/format/html/format-html-links.ts
+++ b/src/format/html/format-html-links.ts
@@ -112,6 +112,9 @@ export function alternateLinks(
     };
   };
 
+  // Formats renamed by a `{format, text}` entry, so no default link is added for them
+  const renamedFormats = new Set<RenderedFormat>();
+
   let count = 1;
   for (const userLink of userLinks || []) {
     if (typeof userLink === "string") {
@@ -132,6 +135,7 @@ export function alternateLinks(
           f.format.identifier[kTargetFormat] === thatLink.format
         );
         if (rf) {
+          renamedFormats.add(rf);
           // Just push through
           alternateLinks.push(
             alternateLinkForFormat(rf, count, thatLink.text, thatLink.icon),
@@ -159,7 +163,10 @@ export function alternateLinks(
   if (!userLinksHasFormat) {
     formats.forEach((renderedFormat) => {
       const baseFormat = renderedFormat.format.identifier["base-format"];
-      if (!kExcludeFormatUnlessExplicit.includes(baseFormat || "html")) {
+      if (
+        !kExcludeFormatUnlessExplicit.includes(baseFormat || "html") &&
+        !renamedFormats.has(renderedFormat)
+      ) {
         alternateLinks.push(alternateLinkForFormat(renderedFormat, count));
       }
       count++;
diff --git a/tests/docs/smoke-all/2026/11/06/9606-href.qmd b/tests/docs/smoke-all/2026/11/06/9606-href.qmd
new file mode 100644
index 00000000000..7812c9c8a48
--- /dev/null
+++ b/tests/docs/smoke-all/2026/11/06/9606-href.qmd
@@ -0,0 +1,24 @@
+---
+title: "format-links with only an explicit href link"
+format:
+  html:
+    format-links:
+      - text: Quarto
+        href: https://quarto.org/
+        icon: globe
+  typst: default
+  docx: default
+_quarto:
+  tests:
+    html:
+      ensureHtmlElementCount:
+        selectors:
+          - '.quarto-alternate-formats a'
+          - '.quarto-alternate-formats a[href="https://quarto.org/"]'
+          - '.quarto-alternate-formats a[href="9606-href.pdf"]'
+          - '.quarto-alternate-formats a[href="9606-href.docx"]'
+        counts: [3, 1, 1, 1]
+---
+
+`format-links` has a single `{text, href}` link, which names no format.
+It is added on top of the default links, so Typst and docx keep theirs (#9606).
diff --git a/tests/docs/smoke-all/2026/11/06/9606-partial.qmd b/tests/docs/smoke-all/2026/11/06/9606-partial.qmd
new file mode 100644
index 00000000000..bfe0a93403b
--- /dev/null
+++ b/tests/docs/smoke-all/2026/11/06/9606-partial.qmd
@@ -0,0 +1,26 @@
+---
+title: "format-links renaming only some formats"
+format:
+  html:
+    format-links:
+      - format: typst
+        text: PDF
+        icon: file-pdf
+  typst: default
+  docx: default
+_quarto:
+  tests:
+    html:
+      ensureHtmlElementCount:
+        selectors:
+          - '.quarto-alternate-formats a'
+          - '.quarto-alternate-formats a[href="9606-partial.pdf"]'
+          - '.quarto-alternate-formats a[href="9606-partial.docx"]'
+        counts: [2, 1, 1]
+      ensureHtmlElementContents:
+        selectors: ['.quarto-alternate-formats a[href="9606-partial.pdf"]']
+        matches: ['^PDF$']
+---
+
+`format-links` renames the Typst link with a `{format, text, icon}` object and does not mention docx.
+The Typst link is renamed, with no second default link for it, and docx keeps its default link (#9606).
diff --git a/tests/docs/smoke-all/2026/11/06/9606.qmd b/tests/docs/smoke-all/2026/11/06/9606.qmd
new file mode 100644
index 00000000000..1881c1464c9
--- /dev/null
+++ b/tests/docs/smoke-all/2026/11/06/9606.qmd
@@ -0,0 +1,29 @@
+---
+title: "format-links with only `{format, text}` entries"
+format:
+  html:
+    format-links:
+      - format: typst
+        text: PDF
+        icon: file-pdf
+      - format: docx
+        text: Word
+        icon: file-word
+  typst: default
+  docx: default
+_quarto:
+  tests:
+    html:
+      ensureHtmlElementCount:
+        selectors:
+          - '.quarto-alternate-formats a'
+          - '.quarto-alternate-formats a[href="9606.pdf"]'
+          - '.quarto-alternate-formats a[href="9606.docx"]'
+        counts: [2, 1, 1]
+      ensureHtmlElementContents:
+        selectors: ['.quarto-alternate-formats a[href="9606.docx"]']
+        matches: ['^Word$']
+---
+
+`format-links` lists every format as a `{format, text, icon}` object and has no plain string entry.
+Listing a format this way renames its link: "Other Formats" shows only PDF and Word, not the default Typst and MS Word links as well (#9606).